Not really. You get what you ask for. You can try image sequences of course and depending on the image content, e.g. LZW-compressed TIFFs might end up producing very small files, but otherwise there's not realyl much you can do other than buying bigger nad faster drives.
Is there a better & efficent way of doing it?
Indeed there is! First, determine your delivery specifications. Do you really need to deliver video in those large dimensions? If you do not, you can work in the smaller HD.
Next, Your workflow is backwards. You edit first and THEN do the effects. AE's strength lies in creating shots, not in creating program-length shots for use when editing later. You'll probably cut out some of that footage. You're not including the backgrounds, which you should be doing if you're working in AE. You're making HUGE alpha-channeled files, some of which you won't even use! You're wasting render time. You're wasting storage space. It's inefficient.
Edit your project. Then chroma key. There is a perfectly-good chroma keyer in Premiere Pro that you should probably use.
There might be a cheap (in terms of file size) way out for you if you render out 2 sequences of high quality JPEGs from After Effects - 1 for the main video, and 1 for the alpha channel (just a black and white image sequence). Then you have a small-ish sequence that you can key out in Premiere using the black and white sequence as a matte. This is not a recommended workflow.
Like Dave said though, edit first, then key.
I'd cut that up into just the shots you are going to use so you don't waste any time working on or rendering frames that you are not going to work on.
Unless your composite requires advanced features you only have assess to in After Effects I would do the keying in Premiere Pro. I would never ever try and dynamically link an AE project (comp) that was longer than a few seconds because:
- When you use Dynamic Link a second background copy of After Effects opens up to render the comp
- This second copy does not have access to any of the GPU accelerated effects you may be using
- This second copy is limited in the amount of system resources that it can use
- Rendering the shots is going to take at least 2 times longer than rendering a DI (digital intermediate) to a suitable production format and replacing your original footage in Premiere Pro
- AE is NOT an editing app and any attempts to use it as such will slow you down, increase render time, be difficult to make changes, and generally be a pain in the a****
I hope this helps. Premiere Pro's Keyers will do at least as good a job if not a much better job as the keying you see on your local weather report in much less time than AE. The only reason to use AE is to do something that can't be done in Premiere Pro or your NLE of choice.